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Initial GitHub action - misspell-fixer

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Cleaned up a variety of typos and should prevent problems in PR
This commit is contained in:
Geoff Hutchison 2020-04-08 17:11:37 -04:00
parent 686ee22f21
commit f758495218
38 changed files with 92 additions and 72 deletions
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16
.github/workflows/misspell-fixer.yml vendored Normal file
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@ -0,0 +1,16 @@
name: misspell-fixer
on: [push]
jobs:
spelling-check:
name: Spelling Check
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: misspell-fixer check for code and comments
uses: sobolevn/misspell-fixer-action@master
with:
options: '-rsvn include/openbabel src tools'
- uses: peter-evans/create-pull-request@v2.4.4
with:
token: ${{ secrets.GITHUB_TOKEN }}

4
.misspell-fixer.ignore Normal file
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@ -0,0 +1,4 @@
^src/formats/outformat.cpp
^src/formats/gamessformat.cpp
^src/formats/libinchi
^tools/obabel.cpp

6
include/openbabel/bond.h
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@ -89,8 +89,8 @@ namespace OpenBabel
enum StereoFlag {
Wedge = (1<<2), //!< A solid black wedge in 2D representations -- i.e., "up" from the 2D plane
Hash = (1<<3), //!< A dashed "hash" bond in 2D representations -- i.e., "down" from the 2D plane
WedgeOrHash = (1<<11), //!< The bond is either wedge or hash, this is a seperate flag!
CisOrTrans = (1<<12) //!< Indicates the 2D/3D coordinates are accidently cis/trans.
WedgeOrHash = (1<<11), //!< The bond is either wedge or hash, this is a separate flag!
CisOrTrans = (1<<12) //!< Indicates the 2D/3D coordinates are accidentally cis/trans.
};
//! Whether this bond has been visited by a graph algorithm
/** \deprecated Use OBBitVec objects instead to be fully thread-safe. **/
@ -243,7 +243,7 @@ namespace OpenBabel
bool IsHash() { return(HasFlag(OB_HASH_BOND)); }
/**
* @return True if this bond is either a wedge or hash.
* @note: This is a seperate bond type
* @note: This is a separate bond type
* @since version 2.3
*/
bool IsWedgeOrHash() const { return(HasFlag(WedgeOrHash)); }

8
include/openbabel/builder.h
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@ -84,24 +84,24 @@ namespace OpenBabel
/*! Atoms a and b are part of two fragments that are not connected in mol.
* Connect will translate and rotate the fragment that contains b so that
* a and b are seperated by a bond. This bond is also added.
* a and b are separated by a bond. This bond is also added.
* \param mol The molecule to be modified
* \param a Index for atom in fragment that should not be rotated.
* \param b Index for atom in fragment that should be rotated.
* \param newpos Direction for new bond between a and b
* \param bondOrder Bond order of the new bond between a and b.
* \returns true if succesful or fails when failed (most likely cause
* \returns true if successful or fails when failed (most likely cause
* for failing: a and b are in the same fragment, they are connected)
*/
static bool Connect(OBMol &mol, int a, int b, vector3 &newpos, int bondOrder = 1);
/*! Atoms a and b are part of two fragments that are not connected in mol.
* Connect will translate and rotate the fragment that contains b so that
* a and b are seperated by a bond. This bond is also added.
* a and b are separated by a bond. This bond is also added.
* \param mol The molecule to be modified
* \param a Index for atom in fragment that should not be rotated.
* \param b Index for atom in fragment that should be rotated.
* \param bondOrder Bond order of the new bond bewtween a and b.
* \returns true if succesfull or fails when failed (most likely cause
* \returns true if successfull or fails when failed (most likely cause
* for failing: a and b are in the same fragment, they are connected)
*/
static bool Connect(OBMol &mol, int a, int b, int bondOrder = 1);

4
include/openbabel/conformersearch.h
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@ -446,7 +446,7 @@ namespace OpenBabel {
std::vector<int> niche_map; //!< Procide the sharing niche index, given the key inddex
void *d; // Opaque pointer - currently for storing OBRandom* which may be removed in future
bool use_sharing; //!< Wether to use sharing or not.
bool use_sharing; //!< Whether to use sharing or not.
double alpha_share; //!< The alpha parameter in sharing function
double sigma_share; //!< The sigma parameter in sharing function
int nb_niches; //!< The number of dynamic niches to be found
@ -479,7 +479,7 @@ namespace OpenBabel {
* Previous OpenBabel releases contained only methods for finding stable (low
* energy) conformers by using the force fields. The 2.3 release introduces a new
* flexible class (OBConformerSearch) implementing a genetic algorithm. The scoring
* or ranking of conformers is done by a seperate class derived from the abstract
* or ranking of conformers is done by a separate class derived from the abstract
* OBConformerScore class. Reimplementing this class allows for all sorts of scoring
* functions (e.g. RMSD, torson, energy, ... based).
*

16
include/openbabel/forcefield.h
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@ -527,7 +527,7 @@ const double GAS_CONSTANT = 8.31446261815324e-3 / KCAL_TO_KJ; //!< kcal mol^-1
OBMol _mol; //!< Molecule to be evaluated or minimized
bool _init; //!< Used to make sure we only parse the parameter file once, when needed
std::string _parFile; //! < parameter file name
bool _validSetup; //!< was the last call to Setup succesfull
bool _validSetup; //!< was the last call to Setup successfull
double *_gradientPtr; //!< pointer to the gradients (used by AddGradient(), minimization functions, ...)
// logging variables
std::ostream* _logos; //!< Output for logfile
@ -623,13 +623,13 @@ const double GAS_CONSTANT = 8.31446261815324e-3 / KCAL_TO_KJ; //!< kcal mol^-1
virtual bool HasAnalyticalGradients() { return false; }
/*! Setup the forcefield for mol (assigns atom types, charges, etc.). Keep current constraints.
* \param mol The OBMol object that contains the atoms and bonds.
* \return True if succesfull.
* \return True if successfull.
*/
bool Setup(OBMol &mol);
/*! Setup the forcefield for mol (assigns atom types, charges, etc.). Use new constraints.
* \param mol The OBMol object that contains the atoms and bonds.
* \param constraints The OBFFConstraints object that contains the constraints.
* \return True if succesfull.
* \return True if successfull.
*/
bool Setup(OBMol &mol, OBFFConstraints &constraints);
/*! Load the parameters (this function is overloaded by the individual forcefields,
@ -706,26 +706,26 @@ const double GAS_CONSTANT = 8.31446261815324e-3 / KCAL_TO_KJ; //!< kcal mol^-1
/*! Get coordinates for current conformer and attach OBConformerData with energies, forces, ... to mol.
* \param mol The OBMol object to copy the coordinates to (from OBForceField::_mol).
* \return True if succesfull.
* \return True if successfull.
*/
bool GetCoordinates(OBMol &mol);
//! \deprecated Use GetCooordinates instead.
bool UpdateCoordinates(OBMol &mol) {return GetCoordinates(mol); }
/*! Get coordinates for all conformers and attach OBConformerData with energies, forces, ... to mol.
* \param mol The OBMol object to copy the coordinates to (from OBForceField::_mol).
* \return True if succesfull.
* \return True if successfull.
*/
bool GetConformers(OBMol &mol);
//! \deprecated Use GetConformers instead.
bool UpdateConformers(OBMol &mol) { return GetConformers(mol); }
/*! Set coordinates for current conformer.
* \param mol the OBMol object to copy the coordinates from (to OBForceField::_mol).
* \return true if succesfull.
* \return true if successfull.
*/
bool SetCoordinates(OBMol &mol);
/*! Set coordinates for all conformers.
* \param mol The OBMol object to copy the coordinates from (to OBForceField::_mol).
* \return True if succesfull.
* \return True if successfull.
*/
bool SetConformers(OBMol &mol);
/*! Create a grid with spacing @p step and @p padding. Place a probe atom of type probe at every grid point,
@ -983,7 +983,7 @@ const double GAS_CONSTANT = 8.31446261815324e-3 / KCAL_TO_KJ; //!< kcal mol^-1
void PrintVelocities();
/*! Set the stream for logging (can also be &cout for logging to screen).
* \param pos Stream (when pos is 0, std::cout wil be used).
* \return True if succesfull.
* \return True if successfull.
*/
bool SetLogFile(std::ostream *pos);
/*! Set the log level (OBFF_LOGLVL_NONE, OBFF_LOGLVL_LOW, OBFF_LOGLVL_MEDIUM, OBFF_LOGLVL_HIGH).

2
include/openbabel/mcdlutil.h
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@ -26,7 +26,7 @@ GNU General Public License for more details.
1. All atoms, except explicit hydrogens, are replaced with generic ANY_ATOM (matched with any atom in subgraph isomorphisme search)
2. All bonds are replaces with generic ANY_BOND, which can be matched with any bond in molecule
3. All hydrogen are removed, but they are used for search-query and structure atom matching is believed fo be
sucessfukk if chemical structure contains more or equal number of hydrogens, than query. Using explicitly-defined hydrogens
successfukk if chemical structure contains more or equal number of hydrogens, than query. Using explicitly-defined hydrogens
on query enables ones to remove substitutors attachment for atom, which are sterically hidden on templates
if the file will not be found, predefined templates will be used
*/

2
include/openbabel/obconversion.h
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@ -318,7 +318,7 @@ namespace OpenBabel {
/// and will usually followed by a call to Convert().
/// Will set format from file extension if format has not already been set.
/// Files will be opened even if format cannot be determined, but not if file path is empty.
/// \return false if unsucessful.
/// \return false if unsuccessful.
bool OpenInAndOutFiles(std::string infilepath, std::string outfilepath);
/// @brief Sends a message like "2 molecules converted" to clog

4
include/openbabel/query.h
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@ -59,8 +59,8 @@ namespace OpenBabel {
/**
* Constructor.
* @param atomicNum The atomic number for this query atom.
* @param isInRing Specify wether the query atom is in a ring. Default is false.
* @param isAromatic Specify wether the query atom is aromatic. Default is false.
* @param isInRing Specify whether the query atom is in a ring. Default is false.
* @param isAromatic Specify whether the query atom is aromatic. Default is false.
*/
OBQueryAtom(int atomicNum = 6, bool isInRing = false, bool isAromatic = false) :
m_atomicNum(atomicNum), m_isInRing(isInRing), m_isAromatic(isAromatic) {}

2
include/openbabel/rotor.h
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@ -532,7 +532,7 @@ namespace OpenBabel
_fixedatoms.Clear();
}
/**
* Intialize the private OBRotorRules database from a specific file.
* Initialize the private OBRotorRules database from a specific file.
*/
void Init(std::string &fname)
{

2
include/openbabel/spectrophore.h
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@ -498,7 +498,7 @@ Spectrophores&tm; are recommended.
NormalizationOption GetNormalization(void) const;
/** Calling this method starts the calculation of the Spectrophore&tm;.
After succesful calculation, the Spectrophore&tm; is returned as a
After successful calculation, the Spectrophore&tm; is returned as a
standard vector of 48 doubles. The 48 doubles are organised into 4 sets
of 12 doubles each:-
- numbers 01-11: Spectrophore&tm; values calculated from the atomic partial charges;

6
include/openbabel/stereo/stereo.h
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@ -119,7 +119,7 @@ namespace OpenBabel {
enum View
{
ViewFrom = 1, //!< view from the atom (id parameter) towards the center atom
ViewTowards = 2 //!< view from center atom towards the atom (id paramater)
ViewTowards = 2 //!< view from center atom towards the atom (id parameter)
};
/**
@ -982,8 +982,8 @@ namespace OpenBabel {
* - C11: 1 true stereocenter OR 1 para stereocenter
*
* These criteria are analogous to the rules from the Razinger paper on
* stereoisomer generation. Since the existance of stereocenters can depend
* on the existance of other stereocenters (in the ligands), the stereocenters
* stereoisomer generation. Since the existence of stereocenters can depend
* on the existence of other stereocenters (in the ligands), the stereocenters
* are found by iterating until no new stereocenters are found.
*
* @verbatim

2
include/openbabel/xml.h
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@ -91,7 +91,7 @@ namespace OpenBabel
static XMLConversion* GetDerived(OBConversion* pConv, bool ForReading=true);
///Because OBConversion::Convert is still using the unextended OBConversion object
///we need to obtain the conversion paramters from it when requested
///we need to obtain the conversion parameters from it when requested
bool IsLast()
{ return _pConv->IsLast(); }
int GetOutputIndex()

2
src/alias.cpp
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@ -50,7 +50,7 @@ namespace OpenBabel
{
/*
Interprets the alias text and adds atom(s) as appropriate to mol.
Tries the following in turn until one is sucessful:
Tries the following in turn until one is successful:
1) If starts with number treat as isotope+element e.g. 2H
2) Looks up alias in superatom.txt e.g. COOH Pr
3) If of the form Rn stored as a * atom with Atom Class data

2
src/builder.cpp
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@ -1663,7 +1663,7 @@ namespace OpenBabel
success = false; // uncorrected bond
}
// Reperceive non-ring TetrahedralStereos if an inversion occured
// Reperceive non-ring TetrahedralStereos if an inversion occurred
if (inversion) {
sgunits.clear();
for (origth = nonringtetra.begin(); origth != nonringtetra.end(); ++origth)

2
src/canon.cpp
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@ -613,7 +613,7 @@ namespace OpenBabel {
/**
* Indexes for the stereo center neighbor atoms. Tetrahedral centers have
* all neighbor atoms in nbrIndexes1. CisTrans stereo centers store the
* neighbor atoms for each double bond atom seperatly.
* neighbor atoms for each double bond atom separatly.
*/
std::vector<unsigned int> nbrIndexes1, nbrIndexes2;
};

8
src/config.h.cmake
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@ -95,13 +95,13 @@
#endif
#ifdef _MSC_VER
// Supress warning on deprecated functions
// Suppress warning on deprecated functions
#pragma warning(disable : 4996)
// Supress warning that compiler is ignoring C++ exception specification
// Suppress warning that compiler is ignoring C++ exception specification
#pragma warning( disable : 4290 )
// Supress warning on signed/unsigned comparison with < or > (harmless, but maybe should be fixed)
// Suppress warning on signed/unsigned comparison with < or > (harmless, but maybe should be fixed)
#pragma warning( disable : 4018 )
// Supress warning on forcing int etc. value to bool 'true' or 'false' (performance warning)
// Suppress warning on forcing int etc. value to bool 'true' or 'false' (performance warning)
#pragma warning( disable : 4800 )
//
#pragma warning( disable : 4251 )

2
src/descriptor.cpp
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@ -516,7 +516,7 @@ void OBDescriptor::DeleteProperties(OBBase* pOb, const string& DescrList)
bool OBDescriptor::Display(std::string&txt, const char* param, const char* ID)
{
//Use the base class version except when the parameter is a descriptor ID.
//For a paramater which is the matching descriptor set verbose.
//For a parameter which is the matching descriptor set verbose.
//No display for other descriptors.
//Allows babel descriptors HBA1
if(param && FindType(param))

8
src/fingerprints/finger3.cpp
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@ -122,10 +122,10 @@ public:
The pattern will set or clear numbits bits in the fingerprint.
They will be in numoccurrences+1 groups, each containing an approximately
equal number of bits.
The first group of bits will be set if numMatches > numoccurences;
The first group of bits will be set if numMatches > numoccurrences;
The second group will be set if numMatches > numoccurrences - 1;
and so on.
So with a pattern with numbits = 4 and numoccurences = 2,
So with a pattern with numbits = 4 and numoccurrences = 2,
the groups would be 1, 1, and 2 bits.
A molecule with
1 match to the pattern would give 0011
@ -339,8 +339,8 @@ description: SMARTS [occurrences [numbits]]
A bit is set in the fingerprint for ach SMARTS pattern matched.
The optional integer parameters refine this behaviour; the most obvious uses are:
- if <occurrences> is present and greater than its default value of 0, the bit
is set only if the number of matches to the pattern is greater than <occurences>.
- if <occurences> is 0 and <numbits> is greater than its default value of 1, then
is set only if the number of matches to the pattern is greater than <occurrences>.
- if <occurrences> is 0 and <numbits> is greater than its default value of 1, then
the fingerprint has <numbits> bits set if there is a match. This gives greater weight
to the pattern for use in similarity measures like Tanimoto.
- if the parameters are n-1 and n and the number of matches is n,

2
src/formats/lmpdatformat.cpp
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@ -253,7 +253,7 @@ namespace OpenBabel
}
//For now, a simple cube may be the best way to go.
//It may be necessary to set the boxlenght to enforce
//It may be necessary to set the boxlength to enforce
//a density.
const char *boxLn = pConv->IsOption("d",OBConversion::OUTOPTIONS);
double xlo,xhi;

4
src/formats/mdlformat.cpp
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@ -591,7 +591,7 @@ namespace OpenBabel
}
}
// Kekulization is neccessary if an aromatic bond is present
// Kekulization is necessary if an aromatic bond is present
if (needs_kekulization) {
mol.SetAromaticPerceived();
// First of all, set the atoms at the ends of the aromatic bonds to also
@ -1419,7 +1419,7 @@ namespace OpenBabel
int natoms = ReadUIntField(vs[3].c_str());
//int nbonds = ReadUIntField(vs[4].c_str());
//int chiral = ReadUIntField(vs[7].c_str());
//number of s groups, number of 3D contraints, chiral flag and regno not yet implemented
//number of s groups, number of 3D constraints, chiral flag and regno not yet implemented
mol.ReserveAtoms(natoms);
ReadV3000Block(ifs,mol,pConv,true);//go for contained blocks

2
src/formats/mol2format.cpp
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@ -491,7 +491,7 @@ namespace OpenBabel
}
}
// Kekulization is neccessary if an aromatic bond is present
// Kekulization is necessary if an aromatic bond is present
if (needs_kekulization) {
// "de-aromatize" carboxylates and (di)thiocarboxylates
// The typical case (in our test suite anyway) is a carboxylate binding to

22
src/formats/nwchemformat.cpp
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@ -180,7 +180,7 @@ static const char* OPTIMIZATION_END_PATTERN = " Optimization converged";
/**
Method reads coordinates from input stream (ifs) and
writes it into supplied OBMol object (molecule).
Input stream must be set to begining of coordinates
Input stream must be set to beginning of coordinates
table in nwo file. (Line after "Output coordinates...")
Stream will be set at next line after geometry table.
If one of input arguments is NULL method returns without
@ -254,7 +254,7 @@ static const char* OPTIMIZATION_END_PATTERN = " Optimization converged";
/**
Method reads charge, dipole and quadrupole moment from input stream (ifs)
and writes them to supplied OBMol object (molecule)
Input stream must be set to begining of Multipole moment
Input stream must be set to beginning of Multipole moment
section in nwo file. (Line after "Multipole analysis of the density")
Stream will be set to the end of multipole moment section.
*/
@ -330,7 +330,7 @@ static const char* OPTIMIZATION_END_PATTERN = " Optimization converged";
/**
Method reads UV Spectra from input stream (ifs)
and writes them to supplied OBMol object (molecule)
Input stream must be set to begining of TDDFT
Input stream must be set to beginning of TDDFT
calculation in nwo file. (Line after "NWChem TDDFT Module")
Stream will be set to the end of calculation.
*/
@ -383,7 +383,7 @@ static const char* OPTIMIZATION_END_PATTERN = " Optimization converged";
/**
Method reads partial charges from input stream (ifs)
and writes them to supplied OBMol object (molecule)
Input stream must be set to begining of charges
Input stream must be set to beginning of charges
table in nwo file. (Line after "Mulliken analysis of the total density")
Stream will be set at next line after charges table.
If reading charges failed or "molecule" contains
@ -455,7 +455,7 @@ static const char* OPTIMIZATION_END_PATTERN = " Optimization converged";
/**
Method reads orbital information from input stream (ifs)
and writes them to supplied OBMol object (molecule).
Input stream must be set to begining of orbital data
Input stream must be set to beginning of orbital data
section in nwo file. (Line after "... Molecular Orbital Analysis")
Stream will be set at next line after end of orbital section.
*/
@ -524,7 +524,7 @@ static const char* OPTIMIZATION_END_PATTERN = " Optimization converged";
/**
Method reads IRC steps from input stream (ifs)
and writes it to supplied OBMol object (molecule).
Input stream must be set to begining of Minimal Energy
Input stream must be set to beginning of Minimal Energy
Path IRC calculation in nwo file.
(Line after "Gonzalez & Schlegel IRC Optimization")
Method wont work if "molecule" already contains data
@ -583,7 +583,7 @@ static const char* OPTIMIZATION_END_PATTERN = " Optimization converged";
/**
Method reads optimization steps from input stream (ifs)
and writes it to supplied OBMol object (molecule).
Input stream must be set to begining of geometry optimization
Input stream must be set to beginning of geometry optimization
calculation in nwo file. (Line after "NWChem Geometry Optimization")
If no geometry data found then "molecule" wont be changed.
After all stream will be set at the end of calculation.
@ -636,7 +636,7 @@ static const char* OPTIMIZATION_END_PATTERN = " Optimization converged";
If any of arguments are NULL method will quit without changes.
If molecule does not contain geometry data method quits
without changes.
Input stream must be set to begining of frequency
Input stream must be set to beginning of frequency
calculation in nwo file.
(Line after "NWChem Nuclear Hessian and Frequency Analysis")
If vibration data not found then only avalible data will be
@ -739,7 +739,7 @@ static const char* OPTIMIZATION_END_PATTERN = " Optimization converged";
/**
Method reads single point energy and all avalible data from input
stream (ifs) and writes it to supplied OBMol object (molecule)
Input stream must be set to begining of energy calculation
Input stream must be set to beginning of energy calculation
in nwo file. (Line after "NWChem <theory> Module")
If energy not found then "molecule" wont be changed.
*/
@ -777,7 +777,7 @@ static const char* OPTIMIZATION_END_PATTERN = " Optimization converged";
/**
Method reads beads and their energies from NEB calculation from
input stream (ifs) and writes them to supplied OBMol object (molecule)
Input stream must be set to begining of NEB calculation
Input stream must be set to beginning of NEB calculation
in nwo file. (Line after "NWChem Minimum Energy Pathway Program (NEB)")
If method failed then "molecule" wont be changed.
*/
@ -881,7 +881,7 @@ static const char* OPTIMIZATION_END_PATTERN = " Optimization converged";
/**
Method reads beads and their energies from ZTS calculation from
input stream (ifs) and writes them to supplied OBMol object (molecule)
Input stream must be set to begining of ZTS calculation
Input stream must be set to beginning of ZTS calculation
in nwo file. (Line after "@ String method.")
If method failed then "molecule" wont be changed.
*/

2
src/formats/orcaformat.cpp
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@ -725,7 +725,7 @@ namespace OpenBabel
if (pos !=0) return (checkBuffer); // do nothing
while (regexec(&myregex, checkBuffer.c_str(), 1, &pm, REG_EXTENDED) == 0) {
checkBuffer.insert(pm.rm_eo-1, " "); // insert whitespace to seperate the columns
checkBuffer.insert(pm.rm_eo-1, " "); // insert whitespace to separate the columns
}
return (checkBuffer);
}

2
src/formats/pdbformat.cpp
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@ -232,7 +232,7 @@ namespace OpenBabel
if (!mol.NumAtoms()) { // skip the rest of this processing
mol.EndModify();
return ateend; //explictly empty molecules are not invalid
return ateend; //explicitly empty molecules are not invalid
}
resdat.AssignBonds(mol);

2
src/formats/pdbqtformat.cpp
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@ -582,7 +582,7 @@ namespace OpenBabel
for (vector <unsigned int>::iterator it=(*tree.find(i)).second.parents.end(); it != (*tree.find(i)).second.parents.begin(); )
{
--it;
if ((*it)==0) {break;} //do not close the main root; that is closed seperately
if ((*it)==0) {break;} //do not close the main root; that is closed separately
vector <unsigned int>::iterator it_parent=it;
--it_parent;
if ((*tree.find(*it)).second.children.size() == 0)

2
src/formats/rsmiformat.cpp
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@ -249,7 +249,7 @@ namespace OpenBabel
OBFormat* pSmiFormat = OBConversion::FindFormat("SMI");
if(!pSmiFormat)
return false;
pConv->AddOption("smilesonly",OBConversion::OUTOPTIONS);//supresses title and new line
pConv->AddOption("smilesonly",OBConversion::OUTOPTIONS);//suppresses title and new line
pConv->AddOption("c",OBConversion::OUTOPTIONS);//output atom classes if available
OBMol jReactants;

6
src/formats/smilesformat.cpp
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@ -308,7 +308,7 @@ namespace OpenBabel {
// stereochimistry
bool chiralWatch; // set when a tetrahedral atom is read
map<OBAtom*, OBTetrahedralStereo::Config*> _tetrahedralMap; // map of tetrahedral atoms and their data
map<OBBond*, char> _upDownMap; // store the '/' & '\' as they occured in smiles
map<OBBond*, char> _upDownMap; // store the '/' & '\' as they occurred in smiles
map<unsigned int, char> _chiralLonePair; // for atoms with potential chiral lone pairs, remember when the l.p. was encountered
bool squarePlanarWatch; // set when a square planar atom is read
map<OBAtom*, OBSquarePlanarStereo::Config*> _squarePlanarMap;
@ -3187,7 +3187,7 @@ namespace OpenBabel {
* the form of a vector of digit/OBBond* pair. Some of the digits may
* be for newly-opened rings (the matching digit occurs later in the
* SMILES string), and some may be for closing rings (the matching
* digit occured earlier in the string).
* digit occurred earlier in the string).
*
* Canonicalization requires that atoms with more than one digit
* have the digits assigned in a canonical fashion. For example,
@ -3849,7 +3849,7 @@ namespace OpenBabel {
visited |= fragments.back();
}
// Determine symmetry classes for each disconnected fragment seperatly
// Determine symmetry classes for each disconnected fragment separatly
symmetry_classes.resize(mol.NumAtoms());
for (std::size_t i = 0; i < fragments.size(); ++i) {
OBGraphSym gs(&mol, &(fragments[i]));

2
src/formats/smiley.h
View File

@ -2462,7 +2462,7 @@ namespace Smiley {
if (m_str[m_pos] == '.') {
if (m_index == 0)
throw Exception(Exception::SyntaxError, LeadingDot,
"Found dot '.' at begining of pattern", 0, 1);
"Found dot '.' at beginning of pattern", 0, 1);
if (m_pos + 1 >= m_str.size())
throw Exception(Exception::SyntaxError, TrailingDot,
"Found dor '.' at ending of pattern", m_pos - 1, 1);

2
src/formats/xml/cmlformat.cpp
View File

@ -1434,7 +1434,7 @@ namespace OpenBabel
obErrorLog.ThrowError(__FUNCTION__, "Cannot find CMLReact format", obError);
return false;
}
//Disable list option and supress topping and tailing in CMLReactFormat.
//Disable list option and suppress topping and tailing in CMLReactFormat.
_pxmlConv->AddOption("l", OBConversion::OUTOPTIONS);
_pxmlConv->AddOption("ReactionsNotStandalone", OBConversion::OUTOPTIONS);
bool ret = pCMLRFormat->WriteMolecule(pOb,_pxmlConv);

2
src/formats/xml/cmlreactformat.cpp
View File

@ -610,7 +610,7 @@ bool CMLReactFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
if(reaclistPos!=string::npos)
mollistPos = s.find("<moleculeList",reaclistPos+1);
footerPos = s.find("</cml");
if(footerPos==string::npos)// cml tag may have been supressed
if(footerPos==string::npos)// cml tag may have been suppressed
footerPos = s.size();
*_pOut << s.substr(0, reaclistPos) //header
<< s.substr(mollistPos, footerPos-mollistPos) //moleculeList

2
src/mcdlutil.cpp
View File

@ -6050,7 +6050,7 @@ namespace OpenBabel {
1. All atoms, except explicit hydrogens, are replaced with generic ANY_ATOM (matched with any atom in subgraph isomorphisme search)
2. All bonds are replaces with generic ANY_BOND, which can be matched with any bond in molecule
3. All hydrogen are removed, but they are used for search-query and structure atom matching is believed fo be
sucessfukk if chemical structure contains more or equal number of hydrogens, than query. Using explicitly-defined hydrogens
successfukk if chemical structure contains more or equal number of hydrogens, than query. Using explicitly-defined hydrogens
on query enables ones to remove substitutors attachment for atom, which are sterically hidden on templates
if the file will not be found, predefined templates will be used
*/

2
src/mol.cpp
View File

@ -3353,7 +3353,7 @@ namespace OpenBabel
}
}
// Kekulization is neccessary if an aromatic bond is present
// Kekulization is necessary if an aromatic bond is present
if (needs_kekulization) {
this->SetAromaticPerceived();
// First of all, set the atoms at the ends of the aromatic bonds to also

2
src/tokenst.cpp
View File

@ -148,7 +148,7 @@ namespace OpenBabel
return txt;
}
//!Read and discard all characters from input stream upto the occurence of a string
//!Read and discard all characters from input stream upto the occurrence of a string
//! \param ifs The input file stream.
//! \param txt (which is also discarded), or the end of the stream.
//! \returns the stream.

2
tools/obgrep.cpp
View File

@ -222,7 +222,7 @@ int main(int argc,char **argv)
pattern_matched = sp.Match(mol);
// the number of times the match occured may matter
// the number of times the match occurred may matter
if ( ntimes )
{ // ntimes is a positive integer of requested matches
// Here, a match mean a unique match (same set of atoms)

2
tools/obminimize.cpp
View File

@ -232,7 +232,7 @@ int main(int argc,char **argv)
totalSteps++;
if (pFF->DetectExplosion()) {
cerr << "explosion has occured!" << endl;
cerr << "explosion has occurred!" << endl;
conv.Write(&mol, &cout);
return(1);
} else

4
tools/obmm.cpp
View File

@ -346,7 +346,7 @@ int main(int argc,char **argv)
continue;
}
cout << "molecule succesfully loaded." << endl;
cout << "molecule successfully loaded." << endl;
cout << " " << mol.NumAtoms() << " atoms" << endl;
cout << " " << mol.NumBonds() << " bonds" << endl;
@ -382,7 +382,7 @@ int main(int argc,char **argv)
continue;
}
cout << "molecule succesfully saved." << endl;
cout << "molecule successfully saved." << endl;
cout << " " << mol.NumAtoms() << " atoms" << endl;
cout << " " << mol.NumBonds() << " bonds" << endl;

2
tools/obthermo.cpp
View File

@ -214,7 +214,7 @@ int main(int argc,char **argv)
* Set the derivative of the second virial coefficient with temperature for cp calculation\n\n
*
* \b --kj:
* Use Joules instead of Calories in the ouput\n\n
* Use Joules instead of Calories in the output\n\n
*
* \par EXAMPLES
* - View the possible options: